Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Pial surface of both hemispheres as specific ASCII output
by Denny Milakara 27 Jan '10

27 Jan '10

Dear Freesurfers, I wonder if there is a way to output the triangulated pial surface for both hemispheres into a single ASCII file according to OFF-file schema: ---------------------------------- OFF numVertices numFaces numEdges x y z x y z ... numVertices like above NVertices v1 v2 v3 ... vN MVertices v1 v2 v3 ... vM ... numFaces like above --------------------------------- ...where the number of edges is to be ignored. Thank you for your suggestions! Denny Milakara

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Acceptable thresholding levels for cluster simulation?
by Dankner, Nathan (NIH/NIMH) [F] 27 Jan '10

27 Jan '10

Hi all, I have a rather general set of questions regarding the dynamics of the cluster simulation. I recently ran a simulation with 10,000 iterations with the threshold at 2 (.01), and received an output that seemed far too liberal, while when I ran it at 5,000 iterations, it appeared to be reasonable. Is there an interaction between threshold level and p value, such that increasing iterations allow areas of dubious significance to become spuriously significant given low threshold levels? I also am having a hard time determining what is kosher in terms of the threshold. Is .01 too liberal? Is there a general consensus on which level to use?

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Creating a Mask or ROI
by Emily Rogalski 27 Jan '10

27 Jan '10

Hello Group, We would like to create an ROI label in qdec and then run a correlation analysis with another factor to determine the relationship between thinning in the ROI and the measure of interest. Instead of looking at a single value from the ROI we want to look at the correlation across each vertex within the ROI. Basically we want to create a color map of the correlation within the ROI. Is this possible? Thanks, Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Two different covariates
by Jürgen Hänggi 27 Jan '10

27 Jan '10

Dear FS experts We would like to model two covariates, one as DODS and the other one as DOSS. Is it possible to do that with the terminal or do we have to use QDEC? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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a question abourt FS longitudinal stream
by Guang Zeng 26 Jan '10

26 Jan '10

Hi, there, I have a question about FS longitudinal stream, Suppose I have two volumes A and B, B is the copy of A, but has been scaled (say, 1%) at each direction. Both of them have been cross-sectionally processed. If we send them to the FS longitudinal stream, what will happen? For example, if we look at the hippocampal volume of A and B (longitudinal result), Should their percentage difference be around 0% or 3%? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390707/direct/01/

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using MRI_label2volume, and Mri_convert
by Pruce, Benjamin 26 Jan '10

26 Jan '10

Hello, I am learning how to use Freesurfer command utilities and I came upon an issue. I have run a subject T1 scan through the recon-all steps and now have my parcel maps. Can someone help direct me on how I can extract individual images for each ROI label in the wmparc.mgz file? I would like to then convert these images to .nii format to read into other software for my analysis. I have performed this process with reading the .mgz into Slicer and doing it by hand(threshold image), but I assume there is a faster, less tedious way to do it using the native commands in Freesurfer. Any help or direction would be greatly appreciated. Best, Ben -- Benjamin Pruce, R.A. Psychological and Brain Sciences Indiana University Bloomington, IN 47401

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FDR Advice
by Emily Rogalski 26 Jan '10

26 Jan '10

We are working with a group of patients that have a focal neurdegenerative dementia that targets the left hemisphere language network. Using FreeSurfer were are able to locate a significant cortical thinning predominantly located within the left hemisphere language regions. We are interested in correlating the degree of thinning, caused by disease, with neuropsychological performance in the patient group (n=20). >From a statistical standpoint its unclear which approach would be best: 1) Should we limit our correlation analysis to the regions that demonstrate significant thinning? If so, what threshold or FDR correction is most appropriate? For example, we can create group thickness maps (Controls vs Patients) using qdec and make our FDR correction extremely stringent at 0.0001 and then create ROI labels based on the thinning that survives (see attached picture). The mean thickness value from each ROI can then be used in a correlation analysis. Does this make sense from a statistical standpoint? or we should we use a less stringent FDR and have a larger region of atrophy? 2) or Should examine correlations across each vertex of the hemisphere using qdec? If so, what threshold or FDR correction is most appropriate? Thanks in advance for your help. Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Re: [Freesurfer] Updating stats from 4.2 to 4.5
by Judith Segall 26 Jan '10

26 Jan '10

Hi Freesurfer community. We have run several hundred subjects though freesurfer using version 4.2 with additional bug patches for the aparcstats2table bug. We would like to update our stats from aparc.a2005s to the aparc.a2009s atlas. Is this possible? If so, what is the appropriate command? Is this methodologically sound? Aside from longitudinal analysis streams, I am not seeing any large differences between 4.2 and 4.5, but wanted to make sure. Thanks for help on this. - Judith S Mind Research Network

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-autorecon-all error
by Evangelou, Iordanis (NIH/NINDS) [E] 26 Jan '10

26 Jan '10

Hi all I am using freesurfer 4.5.0 and i get the following message after i execute recon-all -s 10272009 -autorecon-all #@# Nu Intensity Correction Tue Jan 26 08:18:31 EST 2010 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl ERROR: flag opening not recognized #-------------------------------------------- #@# Talairach Tue Jan 26 08:18:31 EST 2010 /home/evangeloui/freesurfer/subjects/10272009/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl opening /usr/local/freesurfer-4.5.0/FreeSurferEnv.ninds Setting=up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME=/usr/local/freesurfer-4.5.0 FSFAST_HOME=/usr/local/freesurfer-4.5.0/fsfast FSF_OUTPUT_FORMAT=nii SUBJECTS_DIR=/home/evangeloui/freesurfer/subjects MNI_DIR=/usr/local/freesurfer-4.5.0/mni FSL_DIR=/usr/local/fsl ERROR: flag opening not recognized cp transforms/talairach.auto.xfm transforms/talairach.xfm cp: cannot stat `transforms/talairach.auto.xfm': No such file or directory any help would be appreciated thanks ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Staff Scientist Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892

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Using Clusters as ROIs
by Dankner, Nathan (NIH/NIMH) [F] 25 Jan '10

25 Jan '10

Hello all, I sent this last week but I think it may have slipped through the cracks. I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help, Nathan

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Freesurfer January 2010